Starting phenix.real_space_refine
on Sat Aug 23 09:37:35 2025 by dcliebschner
===============================================================================

Processing files:
-------------------------------------------------------------------------------

  Found model, /net/cci-nas-00/data/ceres_data/5zak_6904/08_2025/5zak_6904.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/5zak_6904/08_2025/5zak_6904.map

Processing PHIL parameters:
-------------------------------------------------------------------------------

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/5zak_6904/08_2025/5zak_6904.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/5zak_6904/08_2025/5zak_6904.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/5zak_6904/08_2025/5zak_6904.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/5zak_6904/08_2025/5zak_6904.map"
  }
  resolution = 4.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.004
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      66      5.16       5
     C    7087      2.51       5
     N    1906      2.21       5
     O    2053      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 11112
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 10552
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1314, 10552
          Classifications: {'peptide': 1314}
          Link IDs: {'CIS': 21, 'PCIS': 4, 'PTRANS': 64, 'TRANS': 1224}
          Chain breaks: 8
    Chain: "B"
      Number of atoms: 560
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 75, 560
          Classifications: {'peptide': 75}
          Link IDs: {'PCIS': 2, 'TRANS': 72}
  Time building chain proxies: 2.96, per 1000 atoms: 0.27
  Number of scatterers: 11112
  At special positions: 0
  Unit cell: (109.749, 104.523, 162.011, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      66     16.00
     O    2053      8.00
     N    1906      7.00
     C    7087      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 196 " - pdb=" SG  CYS A 199 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 443 " - pdb=" SG  CYS A 531 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.03
  Conformation dependent library (CDL) restraints added in 546.2 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  2738 Ramachandran restraints generated.
    1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2666

  Finding SS restraints...
    Secondary structure from input PDB file:
      50 helices and 8 sheets defined
      47.9% alpha, 5.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.41
  Creating SS restraints...
    Processing helix  chain 'A' and resid 45 through 54
    Processing helix  chain 'A' and resid 69 through 85
      removed outlier: 3.850A  pdb=" N   ILE A  73 " --> pdb=" O   GLY A  69 " (cutoff:3.500A)
      removed outlier: 3.751A  pdb=" N   TYR A  83 " --> pdb=" O   LYS A  79 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 102 through 115
      removed outlier: 4.526A  pdb=" N   THR A 115 " --> pdb=" O   SER A 111 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 151 through 159
      removed outlier: 3.651A  pdb=" N   LEU A 156 " --> pdb=" O   CYS A 152 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 176 through 180
    Processing helix  chain 'A' and resid 185 through 194
    Processing helix  chain 'A' and resid 218 through 231
    Processing helix  chain 'A' and resid 264 through 285
      removed outlier: 4.486A  pdb=" N   ASN A 285 " --> pdb=" O   ILE A 281 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 295 through 314
      removed outlier: 4.314A  pdb=" N   SER A 299 " --> pdb=" O   SER A 295 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 314 through 336
      removed outlier: 3.821A  pdb=" N   ALA A 318 " --> pdb=" O   GLY A 314 " (cutoff:3.500A)
      removed outlier: 4.248A  pdb=" N   LYS A 331 " --> pdb=" O   ARG A 327 " (cutoff:3.500A)
      removed outlier: 3.717A  pdb=" N   TYR A 332 " --> pdb=" O   GLU A 328 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 338 through 359
    Processing helix  chain 'A' and resid 377 through 386
    Processing helix  chain 'A' and resid 451 through 461
      removed outlier: 3.642A  pdb=" N   VAL A 455 " --> pdb=" O   ARG A 451 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 497 through 510
      removed outlier: 3.585A  pdb=" N   GLN A 501 " --> pdb=" O   GLU A 497 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 510 through 516
      removed outlier: 3.548A  pdb=" N   ASN A 514 " --> pdb=" O   ALA A 510 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 542 through 551
    Processing helix  chain 'A' and resid 570 through 590
      removed outlier: 4.327A  pdb=" N   ASN A 588 " --> pdb=" O   LYS A 584 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 630 through 639
      removed outlier: 3.723A  pdb=" N   TYR A 637 " --> pdb=" O   HIS A 633 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 686 through 704
    Processing helix  chain 'A' and resid 713 through 726
      removed outlier: 4.340A  pdb=" N   LYS A 717 " --> pdb=" O   MET A 713 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 794 through 798
      removed outlier: 3.967A  pdb=" N   ASP A 797 " --> pdb=" O   PRO A 794 " (cutoff:3.500A)
      removed outlier: 4.026A  pdb=" N   THR A 798 " --> pdb=" O   PRO A 795 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 794 through 798'
    Processing helix  chain 'A' and resid 839 through 855
    Processing helix  chain 'A' and resid 894 through 903
      removed outlier: 3.766A  pdb=" N   GLU A 898 " --> pdb=" O   PHE A 894 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   SER A 903 " --> pdb=" O   ASP A 899 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 904 through 907
      removed outlier: 4.091A  pdb=" N   ILE A 907 " --> pdb=" O   GLU A 904 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 904 through 907'
    Processing helix  chain 'A' and resid 923 through 927
    Processing helix  chain 'A' and resid 967 through 975
      removed outlier: 3.943A  pdb=" N   TYR A 971 " --> pdb=" O   THR A 967 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1002 through 1010
    Processing helix  chain 'A' and resid 1015 through 1031
      removed outlier: 3.987A  pdb=" N   GLN A1031 " --> pdb=" O   LEU A1027 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1044 through 1052
    Processing helix  chain 'A' and resid 1053 through 1072
      removed outlier: 3.776A  pdb=" N   CYS A1063 " --> pdb=" O   TYR A1059 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1294 through 1302
    Processing helix  chain 'A' and resid 1312 through 1333
      removed outlier: 4.522A  pdb=" N   SER A1321 " --> pdb=" O   MET A1317 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1339 through 1352
    Processing helix  chain 'A' and resid 1352 through 1362
      removed outlier: 3.702A  pdb=" N   LYS A1362 " --> pdb=" O   ARG A1358 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1363 through 1368
      Proline residue:  A1366  - end of helix
      No H-bonds generated for 'chain 'A' and resid 1363 through 1368'
    Processing helix  chain 'A' and resid 1558 through 1574
    Processing helix  chain 'A' and resid 1575 through 1587
      removed outlier: 4.730A  pdb=" N   ALA A1579 " --> pdb=" O   GLY A1575 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1594 through 1599
    Processing helix  chain 'A' and resid 1656 through 1674
      removed outlier: 3.873A  pdb=" N   GLY A1665 " --> pdb=" O   HIS A1661 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   GLU A1667 " --> pdb=" O   ILE A1663 " (cutoff:3.500A)
      removed outlier: 4.232A  pdb=" N   ASN A1668 " --> pdb=" O   SER A1664 " (cutoff:3.500A)
      removed outlier: 3.971A  pdb=" N   PHE A1669 " --> pdb=" O   GLY A1665 " (cutoff:3.500A)
      removed outlier: 4.119A  pdb=" N   LYS A1672 " --> pdb=" O   ASN A1668 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1679 through 1687
      removed outlier: 4.092A  pdb=" N   LEU A1683 " --> pdb=" O   ASN A1679 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1701 through 1722
      removed outlier: 4.173A  pdb=" N   ALA A1710 " --> pdb=" O   PHE A1706 " (cutoff:3.500A)
      removed outlier: 3.772A  pdb=" N   ILE A1711 " --> pdb=" O   LEU A1707 " (cutoff:3.500A)
      removed outlier: 3.897A  pdb=" N   ASP A1713 " --> pdb=" O   ASP A1709 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1728 through 1739
    Processing helix  chain 'A' and resid 1741 through 1752
      removed outlier: 3.825A  pdb=" N   PHE A1745 " --> pdb=" O   ASN A1741 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1762 through 1774
      removed outlier: 3.566A  pdb=" N   PHE A1766 " --> pdb=" O   SER A1762 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1805 through 1823
      removed outlier: 4.164A  pdb=" N   GLY A1809 " --> pdb=" O   PRO A1805 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1826 through 1845
      Proline residue:  A1836  - end of helix
      Proline residue:  A1840  - end of helix
    Processing helix  chain 'A' and resid 1853 through 1858
    Processing helix  chain 'A' and resid 1896 through 1911
    Processing helix  chain 'B' and resid 293 through 305
      removed outlier: 3.876A  pdb=" N   VAL B 297 " --> pdb=" O   ALA B 293 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 343 through 362
    Processing sheet with id=AA1, first strand: chain 'A' and resid 61 through 63
      removed outlier: 8.656A  pdb=" N   LEU A 172 " --> pdb=" O   LEU A 203 " (cutoff:3.500A)
      removed outlier: 9.417A  pdb=" N   LEU A 205 " --> pdb=" O   LEU A 172 " (cutoff:3.500A)
      removed outlier: 6.626A  pdb=" N   VAL A  97 " --> pdb=" O   VAL A 173 " (cutoff:3.500A)
      removed outlier: 7.750A  pdb=" N   PHE A  98 " --> pdb=" O   MET A 150 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 250 through 251
      removed outlier: 5.807A  pdb=" N   VAL A 534 " --> pdb=" O   ILE A 561 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 474 through 475
      removed outlier: 3.705A  pdb=" N   HIS A 482 " --> pdb=" O   SER A 475 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 829 through 836
      removed outlier: 6.595A  pdb=" N   LEU A 770 " --> pdb=" O   LYS A 832 " (cutoff:3.500A)
      removed outlier: 5.240A  pdb=" N   SER A 834 " --> pdb=" O   CYS A 768 " (cutoff:3.500A)
      removed outlier: 6.759A  pdb=" N   CYS A 768 " --> pdb=" O   SER A 834 " (cutoff:3.500A)
      removed outlier: 4.076A  pdb=" N   PHE A 802 " --> pdb=" O   ILE A 773 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 776 through 780
      removed outlier: 6.632A  pdb=" N   GLU A 824 " --> pdb=" O   THR A 778 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 990 through 992
      removed outlier: 4.581A  pdb=" N   ALA A 930 " --> pdb=" O   VAL A 947 " (cutoff:3.500A)
      removed outlier: 4.050A  pdb=" N   VAL A 931 " --> pdb=" O   HIS A1041 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 1882 through 1884
    Processing sheet with id=AA8, first strand: chain 'B' and resid 324 through 328

    465 hydrogen bonds defined for protein.
    1368 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.02

  Time building geometry restraints manager: 1.29 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        1.21 -     1.33: 3053
        1.33 -     1.46: 2476
        1.46 -     1.58: 5712
        1.58 -     1.70: 1
        1.70 -     1.83: 90
  Bond restraints: 11332
  Sorted by residual:
  bond pdb=" N   LYS A 862 "
       pdb=" CA  LYS A 862 "
    ideal  model  delta    sigma   weight residual
    1.455  1.486 -0.031 9.60e-03 1.09e+04 1.04e+01
  bond pdb=" CA  VAL A1804 "
       pdb=" C   VAL A1804 "
    ideal  model  delta    sigma   weight residual
    1.522  1.543 -0.021 7.10e-03 1.98e+04 8.97e+00
  bond pdb=" N   LYS A1589 "
       pdb=" CA  LYS A1589 "
    ideal  model  delta    sigma   weight residual
    1.461  1.494 -0.033 1.20e-02 6.94e+03 7.66e+00
  bond pdb=" N   LYS A 135 "
       pdb=" CA  LYS A 135 "
    ideal  model  delta    sigma   weight residual
    1.458  1.507 -0.049 1.90e-02 2.77e+03 6.67e+00
  bond pdb=" C   MET A 713 "
       pdb=" N   PRO A 714 "
    ideal  model  delta    sigma   weight residual
    1.336  1.368 -0.032 1.25e-02 6.40e+03 6.54e+00
  ... (remaining 11327 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.40: 14621
        3.40 -     6.80: 578
        6.80 -    10.19: 92
       10.19 -    13.59: 24
       13.59 -    16.99: 8
  Bond angle restraints: 15323
  Sorted by residual:
  angle pdb=" C   THR A 134 "
        pdb=" N   LYS A 135 "
        pdb=" CA  LYS A 135 "
      ideal   model   delta    sigma   weight residual
     121.70  137.95  -16.25 1.80e+00 3.09e-01 8.15e+01
  angle pdb=" C   HIS A 116 "
        pdb=" N   SER A 117 "
        pdb=" CA  SER A 117 "
      ideal   model   delta    sigma   weight residual
     121.70  136.76  -15.06 1.80e+00 3.09e-01 7.00e+01
  angle pdb=" C   LEU A 649 "
        pdb=" N   ALA A 650 "
        pdb=" CA  ALA A 650 "
      ideal   model   delta    sigma   weight residual
     121.70  135.01  -13.31 1.80e+00 3.09e-01 5.47e+01
  angle pdb=" C   ARG A 137 "
        pdb=" N   TRP A 138 "
        pdb=" CA  TRP A 138 "
      ideal   model   delta    sigma   weight residual
     121.70  134.41  -12.71 1.80e+00 3.09e-01 4.99e+01
  angle pdb=" C   GLU A1551 "
        pdb=" N   GLN A1552 "
        pdb=" CA  GLN A1552 "
      ideal   model   delta    sigma   weight residual
     121.70  134.32  -12.62 1.80e+00 3.09e-01 4.92e+01
  ... (remaining 15318 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.24: 6453
       17.24 -    34.47: 460
       34.47 -    51.71: 60
       51.71 -    68.94: 2
       68.94 -    86.18: 4
  Dihedral angle restraints: 6979
    sinusoidal: 2876
      harmonic: 4103
  Sorted by residual:
  dihedral pdb=" CA  PRO A1376 "
           pdb=" C   PRO A1376 "
           pdb=" N   PRO A1377 "
           pdb=" CA  PRO A1377 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -135.70  -44.30     0      5.00e+00 4.00e-02 7.85e+01
  dihedral pdb=" CA  ALA A 207 "
           pdb=" C   ALA A 207 "
           pdb=" N   SER A 208 "
           pdb=" CA  SER A 208 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -139.53  -40.47     0      5.00e+00 4.00e-02 6.55e+01
  dihedral pdb=" CA  SER A 165 "
           pdb=" C   SER A 165 "
           pdb=" N   LEU A 166 "
           pdb=" CA  LEU A 166 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -141.53  -38.47     0      5.00e+00 4.00e-02 5.92e+01
  ... (remaining 6976 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.068: 1201
       0.068 -    0.136: 443
       0.136 -    0.204: 80
       0.204 -    0.272: 17
       0.272 -    0.340: 6
  Chirality restraints: 1747
  Sorted by residual:
  chirality pdb=" CB  ILE A 479 "
            pdb=" CA  ILE A 479 "
            pdb=" CG1 ILE A 479 "
            pdb=" CG2 ILE A 479 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.30    0.34 2.00e-01 2.50e+01 2.89e+00
  chirality pdb=" CG  LEU A 865 "
            pdb=" CB  LEU A 865 "
            pdb=" CD1 LEU A 865 "
            pdb=" CD2 LEU A 865 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.26   -0.33 2.00e-01 2.50e+01 2.76e+00
  chirality pdb=" CB  ILE A 813 "
            pdb=" CA  ILE A 813 "
            pdb=" CG1 ILE A 813 "
            pdb=" CG2 ILE A 813 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.34    0.31 2.00e-01 2.50e+01 2.37e+00
  ... (remaining 1744 not shown)

  Planarity restraints: 1954
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO A 682 "   -0.063 5.00e-02 4.00e+02   9.57e-02 1.47e+01
        pdb=" N   PRO A 683 "    0.166 5.00e-02 4.00e+02
        pdb=" CA  PRO A 683 "   -0.051 5.00e-02 4.00e+02
        pdb=" CD  PRO A 683 "   -0.052 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 637 "    0.036 2.00e-02 2.50e+03   2.57e-02 1.32e+01
        pdb=" CG  TYR A 637 "   -0.061 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 637 "    0.003 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 637 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 637 "    0.007 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 637 "    0.012 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 637 "    0.004 2.00e-02 2.50e+03
        pdb=" OH  TYR A 637 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER A1664 "   -0.016 2.00e-02 2.50e+03   3.26e-02 1.06e+01
        pdb=" C   SER A1664 "    0.056 2.00e-02 2.50e+03
        pdb=" O   SER A1664 "   -0.021 2.00e-02 2.50e+03
        pdb=" N   GLY A1665 "   -0.019 2.00e-02 2.50e+03
  ... (remaining 1951 not shown)

  Histogram of nonbonded interaction distances:
        2.18 -     2.73: 933
        2.73 -     3.27: 11569
        3.27 -     3.81: 19692
        3.81 -     4.36: 24072
        4.36 -     4.90: 37002
  Nonbonded interactions: 93268
  Sorted by model distance:
  nonbonded pdb=" O   LEU A1684 "
            pdb=" OG1 THR A1688 "
     model   vdw
     2.185 3.040
  nonbonded pdb=" O   VAL A  75 "
            pdb=" OG1 THR A  78 "
     model   vdw
     2.197 3.040
  nonbonded pdb=" OG1 THR B 331 "
            pdb=" O   PRO B 333 "
     model   vdw
     2.211 3.040
  nonbonded pdb=" OD2 ASP A 283 "
            pdb=" OG  SER B 318 "
     model   vdw
     2.226 3.040
  nonbonded pdb=" O   SER A1868 "
            pdb=" OH  TYR A1897 "
     model   vdw
     2.238 3.040
  ... (remaining 93263 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.420
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.170
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     11.920
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.580
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.230
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6491
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.095  11334  Z= 0.420
  Angle     :  1.607  16.991  15327  Z= 0.871
  Chirality :  0.073   0.340   1747
  Planarity :  0.010   0.096   1954
  Dihedral  : 11.718  86.176   4307
  Min Nonbonded Distance : 2.185

Molprobity Statistics.
  All-atom Clashscore : 17.87
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  : 17.31 %
    Favored  : 82.40 %
  Rotamer:
    Outliers :  0.72 %
    Allowed  :  3.22 %
    Favored  : 96.05 %
  Cbeta Deviations :  0.08 %
  Peptide Plane:
    Cis-proline     : 8.57 %
    Cis-general     : 1.60 %
    Twisted Proline : 2.86 %
    Twisted General : 0.84 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -5.20 (0.18), residues: 1369
  helix: -3.01 (0.15), residues: 576
  sheet: -3.81 (0.40), residues: 97
  loop : -3.86 (0.21), residues: 696

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG A 640 
 TYR   0.061   0.005   TYR A 637 
 PHE   0.042   0.005   PHE A 537 
 TRP   0.030   0.005   TRP A 133 
 HIS   0.021   0.004   HIS A 703 

Details of bonding type rmsd
  covalent geometry    : bond        0.00886 (11332)
  covalent geometry    : angle       1.60674 (15323)
  SS BOND              : bond        0.00683 (    2)
  SS BOND              : angle       3.06336 (    4)
  hydrogen bonds       : bond        0.17211 (  465)
  hydrogen bonds       : angle       9.29059 ( 1368)

*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2738 Ramachandran restraints generated.
    1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2738 Ramachandran restraints generated.
    1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  275 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 266
  time to evaluate  : 0.267 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   64 LEU cc_start: 0.7747 (tp) cc_final: 0.7478 (tp)
REVERT: A   80 GLU cc_start: 0.8731 (tt0) cc_final: 0.8280 (tp30)
REVERT: A  190 MET cc_start: 0.8634 (ttp) cc_final: 0.8380 (tmm)
REVERT: A  218 GLU cc_start: 0.9131 (pt0) cc_final: 0.8917 (pt0)
REVERT: A  224 GLN cc_start: 0.8815 (tt0) cc_final: 0.8379 (tm-30)
REVERT: A  239 ASP cc_start: 0.5620 (m-30) cc_final: 0.5400 (m-30)
REVERT: A  458 ASN cc_start: 0.6512 (t0) cc_final: 0.6216 (t0)
REVERT: A  479 ILE cc_start: 0.3082 (OUTLIER) cc_final: 0.2733 (mp)
REVERT: A  560 TYR cc_start: 0.7210 (t80) cc_final: 0.6847 (t80)
REVERT: A  580 LYS cc_start: 0.9197 (ttpt) cc_final: 0.8944 (tppt)
REVERT: A  697 ILE cc_start: 0.7652 (mt) cc_final: 0.6962 (mt)
REVERT: A 1313 GLU cc_start: 0.8095 (mt-10) cc_final: 0.7708 (mm-30)
REVERT: A 1327 ILE cc_start: 0.8175 (mm) cc_final: 0.7849 (pt)
REVERT: A 1346 MET cc_start: 0.7857 (mmm) cc_final: 0.7622 (mmm)
REVERT: A 1358 ARG cc_start: 0.7458 (mtt180) cc_final: 0.7180 (mtt-85)
REVERT: A 1363 LYS cc_start: 0.8667 (mmtt) cc_final: 0.8432 (mmmt)
REVERT: A 1564 GLU cc_start: 0.8937 (mt-10) cc_final: 0.8658 (mt-10)
REVERT: A 1576 GLU cc_start: 0.8692 (tt0) cc_final: 0.8415 (mm-30)
REVERT: A 1687 PHE cc_start: 0.8364 (m-80) cc_final: 0.7819 (m-80)
REVERT: A 1692 TYR cc_start: 0.7894 (t80) cc_final: 0.7443 (t80)
REVERT: A 1705 GLU cc_start: 0.7121 (tt0) cc_final: 0.6527 (tt0)
REVERT: A 1768 VAL cc_start: 0.7740 (t) cc_final: 0.7374 (p)
REVERT: A 1772 PHE cc_start: 0.6296 (t80) cc_final: 0.5961 (t80)
REVERT: A 1782 MET cc_start: 0.4860 (mmt) cc_final: 0.4395 (mpp)
REVERT: A 1810 ASP cc_start: 0.6632 (m-30) cc_final: 0.6174 (t0)
REVERT: A 1813 GLU cc_start: 0.6942 (mt-10) cc_final: 0.6640 (mm-30)
REVERT: A 1825 MET cc_start: 0.7483 (mtt) cc_final: 0.7105 (mtm)
REVERT: B  353 ARG cc_start: 0.8378 (ttp80) cc_final: 0.8116 (ttp80)
  outliers start: 9
  outliers final: 1
  residues processed: 273
  average time/residue: 0.1320
  time to fit residues: 47.3072
Evaluate side-chains
  156 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 154
  time to evaluate  : 0.423 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 98 optimal weight:    1.9990
   chunk 107 optimal weight:    3.9990
   chunk 10 optimal weight:    5.9990
   chunk 66 optimal weight:    0.8980
   chunk 130 optimal weight:    5.9990
   chunk 124 optimal weight:    0.6980
   chunk 103 optimal weight:    0.5980
   chunk 77 optimal weight:    1.9990
   chunk 122 optimal weight:    1.9990
   chunk 91 optimal weight:    5.9990
   chunk 55 optimal weight:    4.9990
   overall best weight:    1.2384

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A  92 ASN
A 101 ASN
** A 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 928 GLN
A1029 ASN
A1041 HIS
A1305 ASN
** A1614 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1661 HIS
A1774 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4237 r_free = 0.4237 target = 0.089598 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.069855 restraints weight = 75431.980|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3848 r_free = 0.3848 target = 0.071958 restraints weight = 53762.410|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3880 r_free = 0.3880 target = 0.073532 restraints weight = 41536.487|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3906 r_free = 0.3906 target = 0.074764 restraints weight = 34041.945|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3922 r_free = 0.3922 target = 0.075609 restraints weight = 28934.185|
|-----------------------------------------------------------------------------|
r_work (final): 0.3932
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6473
moved from start:          0.2896

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  11334  Z= 0.175
  Angle     :  0.955  12.163  15327  Z= 0.496
  Chirality :  0.051   0.312   1747
  Planarity :  0.007   0.082   1954
  Dihedral  :  8.197  34.281   1519
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 23.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.97 %
    Favored  : 85.03 %
  Rotamer:
    Outliers :  0.16 %
    Allowed  :  3.38 %
    Favored  : 96.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.57 %
    Cis-general     : 1.60 %
    Twisted Proline : 1.43 %
    Twisted General : 0.38 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -4.26 (0.20), residues: 1369
  helix: -1.90 (0.18), residues: 610
  sheet: -3.27 (0.40), residues: 126
  loop : -3.72 (0.23), residues: 633

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 821 
 TYR   0.018   0.002   TYR A 972 
 PHE   0.019   0.002   PHE B 307 
 TRP   0.008   0.002   TRP A 316 
 HIS   0.006   0.001   HIS A1661 

Details of bonding type rmsd
  covalent geometry    : bond        0.00361 (11332)
  covalent geometry    : angle       0.95459 (15323)
  SS BOND              : bond        0.00278 (    2)
  SS BOND              : angle       1.97735 (    4)
  hydrogen bonds       : bond        0.05739 (  465)
  hydrogen bonds       : angle       6.89038 ( 1368)

*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2738 Ramachandran restraints generated.
    1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2738 Ramachandran restraints generated.
    1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  223 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 221
  time to evaluate  : 0.335 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   64 LEU cc_start: 0.7507 (tp) cc_final: 0.7165 (tp)
REVERT: A   80 GLU cc_start: 0.8524 (tt0) cc_final: 0.8137 (tp30)
REVERT: A  133 TRP cc_start: 0.7076 (p90) cc_final: 0.6702 (p-90)
REVERT: A  190 MET cc_start: 0.8422 (ttp) cc_final: 0.8146 (tmm)
REVERT: A  218 GLU cc_start: 0.9058 (pt0) cc_final: 0.8830 (pt0)
REVERT: A  224 GLN cc_start: 0.8759 (tt0) cc_final: 0.8297 (tm-30)
REVERT: A  245 ARG cc_start: 0.6924 (mtp-110) cc_final: 0.5983 (tmt170)
REVERT: A  351 PHE cc_start: 0.9122 (t80) cc_final: 0.8892 (t80)
REVERT: A  378 ILE cc_start: 0.8504 (mm) cc_final: 0.8246 (mm)
REVERT: A  458 ASN cc_start: 0.6528 (t0) cc_final: 0.6168 (t0)
REVERT: A  462 LYS cc_start: 0.7765 (mttt) cc_final: 0.7511 (mtmt)
REVERT: A  550 LYS cc_start: 0.7913 (ttpt) cc_final: 0.7542 (pttt)
REVERT: A  560 TYR cc_start: 0.6954 (t80) cc_final: 0.5949 (t80)
REVERT: A  793 TYR cc_start: 0.8075 (m-80) cc_final: 0.7787 (m-80)
REVERT: A 1314 ARG cc_start: 0.6421 (mmm-85) cc_final: 0.5832 (mmm160)
REVERT: A 1317 MET cc_start: 0.8233 (tpp) cc_final: 0.8011 (mtm)
REVERT: A 1346 MET cc_start: 0.7585 (mmm) cc_final: 0.7351 (mmm)
REVERT: A 1564 GLU cc_start: 0.8837 (mt-10) cc_final: 0.8414 (mt-10)
REVERT: A 1668 ASN cc_start: 0.7867 (t0) cc_final: 0.7158 (t0)
REVERT: A 1692 TYR cc_start: 0.7823 (t80) cc_final: 0.7453 (t80)
REVERT: A 1748 LEU cc_start: 0.8831 (mm) cc_final: 0.8471 (tp)
REVERT: A 1772 PHE cc_start: 0.6194 (t80) cc_final: 0.5900 (t80)
REVERT: A 1813 GLU cc_start: 0.6919 (mt-10) cc_final: 0.6538 (mm-30)
REVERT: A 1822 ASP cc_start: 0.7237 (t70) cc_final: 0.7032 (t0)
REVERT: A 1837 MET cc_start: 0.6455 (mtt) cc_final: 0.4699 (mtt)
REVERT: B  311 TYR cc_start: 0.7686 (m-80) cc_final: 0.7366 (m-80)
  outliers start: 2
  outliers final: 0
  residues processed: 221
  average time/residue: 0.1249
  time to fit residues: 37.1672
Evaluate side-chains
  155 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 155
  time to evaluate  : 0.365 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 53 optimal weight:    5.9990
   chunk 79 optimal weight:    4.9990
   chunk 3 optimal weight:    3.9990
   chunk 29 optimal weight:    8.9990
   chunk 92 optimal weight:    8.9990
   chunk 135 optimal weight:    0.9990
   chunk 56 optimal weight:    5.9990
   chunk 7 optimal weight:    5.9990
   chunk 99 optimal weight:    7.9990
   chunk 9 optimal weight:    4.9990
   chunk 35 optimal weight:    3.9990
   overall best weight:    3.7990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 491 ASN
** A1006 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1614 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1660 ASN
A1702 GLN
A1774 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4189 r_free = 0.4189 target = 0.086619 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.067428 restraints weight = 80176.181|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.069469 restraints weight = 56993.946|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3835 r_free = 0.3835 target = 0.070882 restraints weight = 44199.781|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3860 r_free = 0.3860 target = 0.072081 restraints weight = 36471.713|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3878 r_free = 0.3878 target = 0.072949 restraints weight = 31111.735|
|-----------------------------------------------------------------------------|
r_work (final): 0.3863
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6550
moved from start:          0.3365

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.051  11334  Z= 0.235
  Angle     :  1.025  17.077  15327  Z= 0.525
  Chirality :  0.053   0.280   1747
  Planarity :  0.007   0.096   1954
  Dihedral  :  8.040  33.034   1519
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 29.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 16.29 %
    Favored  : 83.71 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  7.09 %
    Favored  : 92.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.57 %
    Cis-general     : 1.60 %
    Twisted Proline : 0.00 %
    Twisted General : 0.38 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.96 (0.20), residues: 1369
  helix: -1.53 (0.19), residues: 610
  sheet: -3.42 (0.41), residues: 108
  loop : -3.67 (0.22), residues: 651

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 640 
 TYR   0.025   0.003   TYR A1752 
 PHE   0.022   0.003   PHE A 854 
 TRP   0.009   0.002   TRP A1831 
 HIS   0.008   0.002   HIS A 703 

Details of bonding type rmsd
  covalent geometry    : bond        0.00501 (11332)
  covalent geometry    : angle       1.02461 (15323)
  SS BOND              : bond        0.00359 (    2)
  SS BOND              : angle       2.47580 (    4)
  hydrogen bonds       : bond        0.06016 (  465)
  hydrogen bonds       : angle       6.84741 ( 1368)

*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2738 Ramachandran restraints generated.
    1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2738 Ramachandran restraints generated.
    1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 184
  time to evaluate  : 0.355 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   64 LEU cc_start: 0.7660 (tp) cc_final: 0.7257 (tp)
REVERT: A  190 MET cc_start: 0.8559 (ttp) cc_final: 0.8251 (tmm)
REVERT: A  218 GLU cc_start: 0.9241 (pt0) cc_final: 0.8838 (pm20)
REVERT: A  224 GLN cc_start: 0.8751 (tt0) cc_final: 0.8308 (tm-30)
REVERT: A  263 ARG cc_start: 0.4742 (tpt90) cc_final: 0.4469 (mtp180)
REVERT: A  550 LYS cc_start: 0.8285 (ttpt) cc_final: 0.7750 (pttt)
REVERT: A  560 TYR cc_start: 0.6838 (t80) cc_final: 0.6044 (t80)
REVERT: A  697 ILE cc_start: 0.7399 (mt) cc_final: 0.6902 (mt)
REVERT: A  701 LYS cc_start: 0.7749 (mmtm) cc_final: 0.7395 (mmtm)
REVERT: A  965 TYR cc_start: 0.9067 (m-80) cc_final: 0.8713 (m-80)
REVERT: A 1311 ASN cc_start: 0.7063 (p0) cc_final: 0.6733 (p0)
REVERT: A 1313 GLU cc_start: 0.7903 (mm-30) cc_final: 0.7422 (mm-30)
REVERT: A 1317 MET cc_start: 0.8210 (tpp) cc_final: 0.7997 (mmt)
REVERT: A 1358 ARG cc_start: 0.7252 (mtt180) cc_final: 0.6734 (mtt-85)
REVERT: A 1564 GLU cc_start: 0.8797 (mt-10) cc_final: 0.8292 (mt-10)
REVERT: A 1664 SER cc_start: 0.7749 (t) cc_final: 0.7477 (p)
REVERT: A 1668 ASN cc_start: 0.7908 (t0) cc_final: 0.7385 (t0)
REVERT: A 1685 GLN cc_start: 0.8809 (tt0) cc_final: 0.8561 (tm-30)
REVERT: A 1692 TYR cc_start: 0.7949 (t80) cc_final: 0.7415 (t80)
REVERT: A 1705 GLU cc_start: 0.6633 (tm-30) cc_final: 0.6430 (tm-30)
REVERT: A 1748 LEU cc_start: 0.8826 (mm) cc_final: 0.8615 (tp)
REVERT: A 1813 GLU cc_start: 0.6812 (mt-10) cc_final: 0.6573 (mm-30)
REVERT: A 1822 ASP cc_start: 0.7413 (t70) cc_final: 0.7212 (t0)
REVERT: A 1837 MET cc_start: 0.7027 (mtt) cc_final: 0.6723 (mtt)
REVERT: A 1860 MET cc_start: 0.1074 (ptm) cc_final: 0.0813 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 184
  average time/residue: 0.1263
  time to fit residues: 31.2595
Evaluate side-chains
  149 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 149
  time to evaluate  : 0.433 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 115 optimal weight:    7.9990
   chunk 39 optimal weight:    0.2980
   chunk 69 optimal weight:    0.9990
   chunk 44 optimal weight:    9.9990
   chunk 53 optimal weight:    0.0030
   chunk 111 optimal weight:    0.9990
   chunk 128 optimal weight:    0.9990
   chunk 16 optimal weight:    7.9990
   chunk 73 optimal weight:   10.0000
   chunk 71 optimal weight:    1.9990
   chunk 49 optimal weight:    8.9990
   overall best weight:    0.6596

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 301 GLN
** A 532 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1614 GLN
** A1689 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4242 r_free = 0.4242 target = 0.090396 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.069805 restraints weight = 77314.815|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3847 r_free = 0.3847 target = 0.072057 restraints weight = 53977.816|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3881 r_free = 0.3881 target = 0.073734 restraints weight = 41275.415|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3905 r_free = 0.3905 target = 0.074936 restraints weight = 33434.234|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3924 r_free = 0.3924 target = 0.075862 restraints weight = 28433.344|
|-----------------------------------------------------------------------------|
r_work (final): 0.3914
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6498
moved from start:          0.4084

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  11334  Z= 0.162
  Angle     :  0.896  13.329  15327  Z= 0.463
  Chirality :  0.049   0.203   1747
  Planarity :  0.006   0.086   1954
  Dihedral  :  7.364  32.619   1519
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 22.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.24 %
    Favored  : 85.76 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.14 %
    Favored  : 96.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.57 %
    Cis-general     : 1.60 %
    Twisted Proline : 0.00 %
    Twisted General : 0.15 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.36 (0.21), residues: 1369
  helix: -0.99 (0.19), residues: 620
  sheet: -2.96 (0.47), residues: 107
  loop : -3.44 (0.23), residues: 642

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A1342 
 TYR   0.018   0.002   TYR A 972 
 PHE   0.026   0.002   PHE A1669 
 TRP   0.008   0.001   TRP A1048 
 HIS   0.005   0.001   HIS A 703 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 (11332)
  covalent geometry    : angle       0.89603 (15323)
  SS BOND              : bond        0.00257 (    2)
  SS BOND              : angle       1.79427 (    4)
  hydrogen bonds       : bond        0.05173 (  465)
  hydrogen bonds       : angle       6.28052 ( 1368)

*********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2738 Ramachandran restraints generated.
    1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2738 Ramachandran restraints generated.
    1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  206 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 206
  time to evaluate  : 0.325 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   64 LEU cc_start: 0.7743 (tp) cc_final: 0.7377 (tp)
REVERT: A   77 LEU cc_start: 0.9242 (mm) cc_final: 0.8870 (mm)
REVERT: A   80 GLU cc_start: 0.8552 (tt0) cc_final: 0.7922 (pt0)
REVERT: A  190 MET cc_start: 0.8442 (ttp) cc_final: 0.8127 (tmm)
REVERT: A  218 GLU cc_start: 0.9083 (pt0) cc_final: 0.8792 (pm20)
REVERT: A  224 GLN cc_start: 0.8698 (tt0) cc_final: 0.8185 (tm-30)
REVERT: A  263 ARG cc_start: 0.4743 (tpt90) cc_final: 0.4422 (mtp180)
REVERT: A  333 ILE cc_start: 0.7096 (mm) cc_final: 0.6867 (mm)
REVERT: A  335 HIS cc_start: 0.8393 (t-90) cc_final: 0.7712 (m170)
REVERT: A  506 ARG cc_start: 0.8267 (ttt180) cc_final: 0.7884 (mmt180)
REVERT: A  550 LYS cc_start: 0.7695 (ttpt) cc_final: 0.7468 (pttt)
REVERT: A  560 TYR cc_start: 0.6374 (t80) cc_final: 0.5476 (t80)
REVERT: A  697 ILE cc_start: 0.7508 (mt) cc_final: 0.7095 (mt)
REVERT: A  965 TYR cc_start: 0.8965 (m-80) cc_final: 0.8569 (m-80)
REVERT: A 1303 LEU cc_start: 0.8712 (tp) cc_final: 0.8239 (tp)
REVERT: A 1313 GLU cc_start: 0.8017 (mm-30) cc_final: 0.7482 (mp0)
REVERT: A 1314 ARG cc_start: 0.6410 (ttt-90) cc_final: 0.6058 (ttt180)
REVERT: A 1317 MET cc_start: 0.7920 (tpp) cc_final: 0.7649 (mmm)
REVERT: A 1337 ASP cc_start: 0.8943 (p0) cc_final: 0.8742 (p0)
REVERT: A 1340 GLU cc_start: 0.6538 (mt-10) cc_final: 0.6088 (mt-10)
REVERT: A 1365 LEU cc_start: 0.9205 (mm) cc_final: 0.8986 (mm)
REVERT: A 1564 GLU cc_start: 0.8778 (mt-10) cc_final: 0.8436 (mt-10)
REVERT: A 1574 CYS cc_start: 0.8722 (m) cc_final: 0.8425 (p)
REVERT: A 1664 SER cc_start: 0.7530 (t) cc_final: 0.7312 (p)
REVERT: A 1668 ASN cc_start: 0.7658 (t0) cc_final: 0.6998 (t0)
REVERT: A 1705 GLU cc_start: 0.6460 (tm-30) cc_final: 0.6116 (tm-30)
REVERT: A 1757 TYR cc_start: 0.6656 (m-80) cc_final: 0.6304 (m-80)
REVERT: A 1813 GLU cc_start: 0.6186 (mt-10) cc_final: 0.5956 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 206
  average time/residue: 0.1343
  time to fit residues: 36.9963
Evaluate side-chains
  148 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 148
  time to evaluate  : 0.398 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 2 optimal weight:    5.9990
   chunk 49 optimal weight:   10.0000
   chunk 80 optimal weight:    9.9990
   chunk 43 optimal weight:   10.0000
   chunk 112 optimal weight:   10.0000
   chunk 16 optimal weight:   10.0000
   chunk 55 optimal weight:    8.9990
   chunk 13 optimal weight:    9.9990
   chunk 118 optimal weight:    0.9980
   chunk 67 optimal weight:    1.9990
   chunk 104 optimal weight:    0.0870
   overall best weight:    3.6164

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 943 HIS
A 998 ASN
** A1006 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1325 HIS
** A1339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4198 r_free = 0.4198 target = 0.086974 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.067785 restraints weight = 77134.687|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.069764 restraints weight = 55160.448|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3852 r_free = 0.3852 target = 0.071283 restraints weight = 42821.051|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 17)----------------|
| r_work = 0.3871 r_free = 0.3871 target = 0.072241 restraints weight = 35309.571|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3886 r_free = 0.3886 target = 0.072972 restraints weight = 30774.167|
|-----------------------------------------------------------------------------|
r_work (final): 0.3879
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6543
moved from start:          0.4261

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040  11334  Z= 0.222
  Angle     :  0.983  13.088  15327  Z= 0.503
  Chirality :  0.052   0.256   1747
  Planarity :  0.007   0.098   1954
  Dihedral  :  7.652  36.592   1519
  Min Nonbonded Distance : 2.413

Molprobity Statistics.
  All-atom Clashscore : 29.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 16.65 %
    Favored  : 83.35 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.22 %
    Favored  : 96.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.57 %
    Cis-general     : 1.60 %
    Twisted Proline : 0.00 %
    Twisted General : 0.31 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.49 (0.21), residues: 1369
  helix: -1.06 (0.19), residues: 619
  sheet: -3.15 (0.40), residues: 125
  loop : -3.51 (0.23), residues: 625

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 640 
 TYR   0.024   0.003   TYR A 637 
 PHE   0.021   0.002   PHE A1772 
 TRP   0.010   0.002   TRP A 133 
 HIS   0.006   0.002   HIS A 633 

Details of bonding type rmsd
  covalent geometry    : bond        0.00473 (11332)
  covalent geometry    : angle       0.98315 (15323)
  SS BOND              : bond        0.00348 (    2)
  SS BOND              : angle       1.66521 (    4)
  hydrogen bonds       : bond        0.05677 (  465)
  hydrogen bonds       : angle       6.44986 ( 1368)

*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2738 Ramachandran restraints generated.
    1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2738 Ramachandran restraints generated.
    1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 186
  time to evaluate  : 0.434 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   64 LEU cc_start: 0.7638 (tp) cc_final: 0.7224 (tp)
REVERT: A   79 LYS cc_start: 0.9291 (mtmm) cc_final: 0.9058 (mtmm)
REVERT: A   80 GLU cc_start: 0.8441 (tt0) cc_final: 0.8167 (tp30)
REVERT: A  190 MET cc_start: 0.8505 (ttp) cc_final: 0.8119 (tmm)
REVERT: A  218 GLU cc_start: 0.9114 (pt0) cc_final: 0.8906 (pt0)
REVERT: A  224 GLN cc_start: 0.8713 (tt0) cc_final: 0.8125 (tm-30)
REVERT: A  263 ARG cc_start: 0.4515 (tpt90) cc_final: 0.4159 (mtp180)
REVERT: A  335 HIS cc_start: 0.8175 (t-90) cc_final: 0.7579 (m170)
REVERT: A  351 PHE cc_start: 0.9037 (t80) cc_final: 0.8824 (t80)
REVERT: A  506 ARG cc_start: 0.8257 (ttt180) cc_final: 0.7849 (mmt180)
REVERT: A  550 LYS cc_start: 0.8304 (ttpt) cc_final: 0.7709 (pttt)
REVERT: A  560 TYR cc_start: 0.6390 (t80) cc_final: 0.5791 (t80)
REVERT: A  697 ILE cc_start: 0.6789 (mt) cc_final: 0.6460 (mt)
REVERT: A  965 TYR cc_start: 0.8953 (m-80) cc_final: 0.8498 (m-80)
REVERT: A 1303 LEU cc_start: 0.8294 (tp) cc_final: 0.8086 (tp)
REVERT: A 1315 LEU cc_start: 0.8202 (mm) cc_final: 0.7954 (mm)
REVERT: A 1337 ASP cc_start: 0.8837 (p0) cc_final: 0.8625 (p0)
REVERT: A 1340 GLU cc_start: 0.6702 (mt-10) cc_final: 0.6488 (mt-10)
REVERT: A 1346 MET cc_start: 0.7110 (mmm) cc_final: 0.6892 (mmm)
REVERT: A 1358 ARG cc_start: 0.7287 (mtt180) cc_final: 0.6737 (mtt-85)
REVERT: A 1564 GLU cc_start: 0.8833 (mt-10) cc_final: 0.8446 (mt-10)
REVERT: A 1574 CYS cc_start: 0.8642 (m) cc_final: 0.8389 (p)
REVERT: A 1664 SER cc_start: 0.7669 (t) cc_final: 0.7385 (p)
REVERT: A 1668 ASN cc_start: 0.7865 (t0) cc_final: 0.7209 (t0)
REVERT: A 1692 TYR cc_start: 0.7878 (t80) cc_final: 0.7670 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 186
  average time/residue: 0.1263
  time to fit residues: 32.1086
Evaluate side-chains
  140 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 140
  time to evaluate  : 0.436 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 115 optimal weight:    5.9990
   chunk 80 optimal weight:    9.9990
   chunk 68 optimal weight:    3.9990
   chunk 45 optimal weight:    5.9990
   chunk 136 optimal weight:    5.9990
   chunk 90 optimal weight:    2.9990
   chunk 0 optimal weight:    8.9990
   chunk 103 optimal weight:    2.9990
   chunk 133 optimal weight:    5.9990
   chunk 122 optimal weight:    4.9990
   chunk 30 optimal weight:    0.8980
   overall best weight:    3.1788

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 301 GLN
A 559 ASN
A 703 HIS
** A 786 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 850 HIS
** A1006 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1031 GLN
** A1339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 338 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4198 r_free = 0.4198 target = 0.086779 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.067633 restraints weight = 77647.852|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.069666 restraints weight = 55275.701|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3849 r_free = 0.3849 target = 0.071197 restraints weight = 42715.695|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3873 r_free = 0.3873 target = 0.072328 restraints weight = 35057.354|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3891 r_free = 0.3891 target = 0.073208 restraints weight = 29972.534|
|-----------------------------------------------------------------------------|
r_work (final): 0.3865
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6528
moved from start:          0.4511

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  11334  Z= 0.207
  Angle     :  0.966  12.458  15327  Z= 0.496
  Chirality :  0.052   0.227   1747
  Planarity :  0.007   0.098   1954
  Dihedral  :  7.598  31.654   1519
  Min Nonbonded Distance : 2.410

Molprobity Statistics.
  All-atom Clashscore : 28.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 16.51 %
    Favored  : 83.49 %
  Rotamer:
    Outliers :  0.08 %
    Allowed  :  2.82 %
    Favored  : 97.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.57 %
    Cis-general     : 1.60 %
    Twisted Proline : 0.00 %
    Twisted General : 0.23 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.47 (0.21), residues: 1369
  helix: -1.12 (0.19), residues: 623
  sheet: -3.20 (0.44), residues: 98
  loop : -3.43 (0.23), residues: 648

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A1342 
 TYR   0.029   0.003   TYR A1834 
 PHE   0.021   0.002   PHE A1745 
 TRP   0.026   0.002   TRP A 133 
 HIS   0.007   0.002   HIS A1062 

Details of bonding type rmsd
  covalent geometry    : bond        0.00437 (11332)
  covalent geometry    : angle       0.96608 (15323)
  SS BOND              : bond        0.00309 (    2)
  SS BOND              : angle       1.63757 (    4)
  hydrogen bonds       : bond        0.05556 (  465)
  hydrogen bonds       : angle       6.43977 ( 1368)

*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2738 Ramachandran restraints generated.
    1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2738 Ramachandran restraints generated.
    1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 181
  time to evaluate  : 0.528 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   64 LEU cc_start: 0.7964 (tp) cc_final: 0.7616 (tp)
REVERT: A   79 LYS cc_start: 0.9270 (mtmm) cc_final: 0.9022 (mtmm)
REVERT: A   80 GLU cc_start: 0.8476 (tt0) cc_final: 0.8195 (tp30)
REVERT: A  190 MET cc_start: 0.8453 (ttp) cc_final: 0.8025 (tmm)
REVERT: A  224 GLN cc_start: 0.8660 (tt0) cc_final: 0.8083 (tm-30)
REVERT: A  263 ARG cc_start: 0.4420 (tpt90) cc_final: 0.4045 (mtp180)
REVERT: A  335 HIS cc_start: 0.8192 (t-90) cc_final: 0.7578 (m170)
REVERT: A  351 PHE cc_start: 0.9075 (t80) cc_final: 0.8851 (t80)
REVERT: A  506 ARG cc_start: 0.8264 (ttt180) cc_final: 0.7876 (mmt180)
REVERT: A  550 LYS cc_start: 0.8253 (ttpt) cc_final: 0.7697 (pttt)
REVERT: A  560 TYR cc_start: 0.6466 (t80) cc_final: 0.5757 (t80)
REVERT: A  572 PHE cc_start: 0.8623 (m-10) cc_final: 0.8356 (m-10)
REVERT: A  965 TYR cc_start: 0.8892 (m-80) cc_final: 0.8416 (m-80)
REVERT: A 1062 HIS cc_start: 0.8827 (p90) cc_final: 0.8523 (t70)
REVERT: A 1315 LEU cc_start: 0.8152 (mm) cc_final: 0.7904 (mm)
REVERT: A 1337 ASP cc_start: 0.8846 (p0) cc_final: 0.8599 (p0)
REVERT: A 1346 MET cc_start: 0.7116 (mmm) cc_final: 0.6900 (mmm)
REVERT: A 1358 ARG cc_start: 0.7284 (mtt180) cc_final: 0.6364 (mtt-85)
REVERT: A 1564 GLU cc_start: 0.8844 (mt-10) cc_final: 0.8479 (mt-10)
REVERT: A 1664 SER cc_start: 0.7749 (t) cc_final: 0.7528 (p)
REVERT: A 1668 ASN cc_start: 0.8009 (t0) cc_final: 0.7486 (t0)
REVERT: A 1682 TYR cc_start: 0.8267 (m-10) cc_final: 0.8008 (m-10)
REVERT: A 1748 LEU cc_start: 0.8789 (mm) cc_final: 0.8425 (tp)
REVERT: A 1837 MET cc_start: 0.6854 (mtt) cc_final: 0.5794 (mtt)
  outliers start: 1
  outliers final: 1
  residues processed: 182
  average time/residue: 0.1227
  time to fit residues: 30.6182
Evaluate side-chains
  133 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 132
  time to evaluate  : 0.460 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 53 optimal weight:    0.6980
   chunk 98 optimal weight:    0.9990
   chunk 130 optimal weight:    2.9990
   chunk 55 optimal weight:    7.9990
   chunk 38 optimal weight:    0.0000
   chunk 107 optimal weight:    5.9990
   chunk 74 optimal weight:    0.1980
   chunk 115 optimal weight:    0.9990
   chunk 10 optimal weight:    3.9990
   chunk 4 optimal weight:    4.9990
   chunk 68 optimal weight:    3.9990
   overall best weight:    0.5788

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 146 GLN
** A 633 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 786 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 338 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4248 r_free = 0.4248 target = 0.090726 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3822 r_free = 0.3822 target = 0.071113 restraints weight = 79134.904|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3866 r_free = 0.3866 target = 0.073235 restraints weight = 55472.508|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3901 r_free = 0.3901 target = 0.074927 restraints weight = 42488.907|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3924 r_free = 0.3924 target = 0.076060 restraints weight = 34445.906|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3942 r_free = 0.3942 target = 0.076978 restraints weight = 29317.332|
|-----------------------------------------------------------------------------|
r_work (final): 0.3971
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6480
moved from start:          0.5055

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  11334  Z= 0.162
  Angle     :  0.911  12.032  15327  Z= 0.467
  Chirality :  0.050   0.224   1747
  Planarity :  0.006   0.089   1954
  Dihedral  :  7.121  33.709   1519
  Min Nonbonded Distance : 2.377

Molprobity Statistics.
  All-atom Clashscore : 20.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 15.63 %
    Favored  : 84.37 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.29 %
    Favored  : 98.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.57 %
    Cis-general     : 1.60 %
    Twisted Proline : 0.00 %
    Twisted General : 0.23 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.08 (0.22), residues: 1369
  helix: -0.73 (0.20), residues: 634
  sheet: -2.47 (0.48), residues: 109
  loop : -3.45 (0.23), residues: 626

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A1342 
 TYR   0.019   0.002   TYR A1692 
 PHE   0.018   0.002   PHE A 347 
 TRP   0.012   0.002   TRP A 133 
 HIS   0.009   0.001   HIS A1062 

Details of bonding type rmsd
  covalent geometry    : bond        0.00331 (11332)
  covalent geometry    : angle       0.91094 (15323)
  SS BOND              : bond        0.00240 (    2)
  SS BOND              : angle       1.33781 (    4)
  hydrogen bonds       : bond        0.04965 (  465)
  hydrogen bonds       : angle       5.98261 ( 1368)

*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2738 Ramachandran restraints generated.
    1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2738 Ramachandran restraints generated.
    1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 193
  time to evaluate  : 0.450 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   48 GLN cc_start: 0.8623 (mt0) cc_final: 0.8408 (pt0)
REVERT: A   64 LEU cc_start: 0.7631 (tp) cc_final: 0.7348 (tp)
REVERT: A   77 LEU cc_start: 0.9251 (mm) cc_final: 0.8989 (mm)
REVERT: A   79 LYS cc_start: 0.9368 (mtmm) cc_final: 0.9144 (mtmm)
REVERT: A   80 GLU cc_start: 0.8602 (tt0) cc_final: 0.8014 (pt0)
REVERT: A  190 MET cc_start: 0.8436 (ttp) cc_final: 0.8047 (tmm)
REVERT: A  224 GLN cc_start: 0.8608 (tt0) cc_final: 0.8047 (tm-30)
REVERT: A  263 ARG cc_start: 0.4923 (tpt90) cc_final: 0.4443 (mtm110)
REVERT: A  279 ASN cc_start: 0.9506 (t0) cc_final: 0.9157 (p0)
REVERT: A  335 HIS cc_start: 0.8210 (t-90) cc_final: 0.7602 (m90)
REVERT: A  458 ASN cc_start: 0.6332 (t0) cc_final: 0.5858 (t0)
REVERT: A  506 ARG cc_start: 0.8217 (ttt180) cc_final: 0.7856 (mmt180)
REVERT: A  560 TYR cc_start: 0.6008 (t80) cc_final: 0.5181 (t80)
REVERT: A  575 ASP cc_start: 0.9178 (m-30) cc_final: 0.8752 (p0)
REVERT: A  697 ILE cc_start: 0.7118 (mt) cc_final: 0.6605 (mt)
REVERT: A  965 TYR cc_start: 0.8914 (m-80) cc_final: 0.8531 (m-80)
REVERT: A  996 ARG cc_start: 0.5800 (ptt180) cc_final: 0.5195 (ptt180)
REVERT: A  998 ASN cc_start: 0.8791 (t0) cc_final: 0.8318 (p0)
REVERT: A 1337 ASP cc_start: 0.8918 (p0) cc_final: 0.8686 (p0)
REVERT: A 1564 GLU cc_start: 0.8725 (mt-10) cc_final: 0.8335 (mt-10)
REVERT: A 1664 SER cc_start: 0.7625 (t) cc_final: 0.7405 (p)
REVERT: A 1668 ASN cc_start: 0.8058 (t0) cc_final: 0.7544 (t0)
REVERT: A 1687 PHE cc_start: 0.8926 (m-80) cc_final: 0.8228 (m-80)
REVERT: A 1692 TYR cc_start: 0.7793 (t80) cc_final: 0.7498 (t80)
REVERT: A 1694 TYR cc_start: 0.7575 (t80) cc_final: 0.7163 (t80)
REVERT: A 1727 HIS cc_start: 0.7150 (m-70) cc_final: 0.6946 (m-70)
REVERT: A 1811 ILE cc_start: 0.7535 (pt) cc_final: 0.7326 (pt)
REVERT: A 1837 MET cc_start: 0.6653 (mtt) cc_final: 0.5632 (mtt)
  outliers start: 0
  outliers final: 0
  residues processed: 193
  average time/residue: 0.1423
  time to fit residues: 36.8614
Evaluate side-chains
  143 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 143
  time to evaluate  : 0.380 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 107 optimal weight:    6.9990
   chunk 3 optimal weight:    0.9990
   chunk 122 optimal weight:    1.9990
   chunk 43 optimal weight:    3.9990
   chunk 64 optimal weight:    0.9990
   chunk 133 optimal weight:   20.0000
   chunk 126 optimal weight:    0.0170
   chunk 45 optimal weight:    0.4980
   chunk 137 optimal weight:    5.9990
   chunk 121 optimal weight:    2.9990
   chunk 0 optimal weight:    8.9990
   overall best weight:    0.9024

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A  84 GLN
** A 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 633 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1693 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4245 r_free = 0.4245 target = 0.090979 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3855 r_free = 0.3855 target = 0.072204 restraints weight = 76473.880|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3895 r_free = 0.3895 target = 0.074235 restraints weight = 55095.474|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3923 r_free = 0.3923 target = 0.075720 restraints weight = 42939.348|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3946 r_free = 0.3946 target = 0.076949 restraints weight = 35593.044|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3964 r_free = 0.3964 target = 0.077842 restraints weight = 30392.809|
|-----------------------------------------------------------------------------|
r_work (final): 0.3956
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6437
moved from start:          0.5353

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  11334  Z= 0.154
  Angle     :  0.894  11.946  15327  Z= 0.457
  Chirality :  0.049   0.228   1747
  Planarity :  0.006   0.079   1954
  Dihedral  :  6.895  31.550   1519
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 21.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 15.12 %
    Favored  : 84.88 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.21 %
    Favored  : 98.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.57 %
    Cis-general     : 1.60 %
    Twisted Proline : 0.00 %
    Twisted General : 0.23 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.87 (0.22), residues: 1369
  helix: -0.56 (0.20), residues: 636
  sheet: -2.21 (0.53), residues: 100
  loop : -3.38 (0.24), residues: 633

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A1314 
 TYR   0.022   0.002   TYR B 358 
 PHE   0.023   0.002   PHE A 347 
 TRP   0.012   0.002   TRP A 133 
 HIS   0.012   0.001   HIS A1062 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 (11332)
  covalent geometry    : angle       0.89394 (15323)
  SS BOND              : bond        0.00258 (    2)
  SS BOND              : angle       1.36777 (    4)
  hydrogen bonds       : bond        0.04781 (  465)
  hydrogen bonds       : angle       5.82592 ( 1368)

*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2738 Ramachandran restraints generated.
    1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2738 Ramachandran restraints generated.
    1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 182
  time to evaluate  : 0.413 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   64 LEU cc_start: 0.7610 (tp) cc_final: 0.7193 (tp)
REVERT: A  190 MET cc_start: 0.8456 (ttp) cc_final: 0.8045 (tmm)
REVERT: A  263 ARG cc_start: 0.4903 (tpt90) cc_final: 0.4431 (mtm110)
REVERT: A  306 CYS cc_start: 0.7017 (m) cc_final: 0.6767 (m)
REVERT: A  335 HIS cc_start: 0.8254 (t-90) cc_final: 0.7553 (m90)
REVERT: A  506 ARG cc_start: 0.8163 (ttt180) cc_final: 0.7801 (mmt180)
REVERT: A  550 LYS cc_start: 0.7963 (ttpt) cc_final: 0.7560 (pttt)
REVERT: A  560 TYR cc_start: 0.5918 (t80) cc_final: 0.5095 (t80)
REVERT: A  575 ASP cc_start: 0.9152 (m-30) cc_final: 0.8813 (p0)
REVERT: A  715 VAL cc_start: 0.7743 (t) cc_final: 0.7414 (t)
REVERT: A  965 TYR cc_start: 0.8944 (m-80) cc_final: 0.8493 (m-80)
REVERT: A  996 ARG cc_start: 0.5480 (ptt180) cc_final: 0.5100 (ptt180)
REVERT: A 1337 ASP cc_start: 0.8964 (p0) cc_final: 0.8709 (p0)
REVERT: A 1346 MET cc_start: 0.7691 (mmm) cc_final: 0.7228 (mmm)
REVERT: A 1358 ARG cc_start: 0.7513 (mtt180) cc_final: 0.7037 (mtt-85)
REVERT: A 1564 GLU cc_start: 0.8654 (mt-10) cc_final: 0.8234 (mt-10)
REVERT: A 1664 SER cc_start: 0.7624 (t) cc_final: 0.7400 (p)
REVERT: A 1668 ASN cc_start: 0.8031 (t0) cc_final: 0.7482 (t0)
REVERT: A 1682 TYR cc_start: 0.8263 (m-10) cc_final: 0.7961 (m-10)
REVERT: A 1692 TYR cc_start: 0.8097 (t80) cc_final: 0.7859 (t80)
REVERT: A 1705 GLU cc_start: 0.6328 (pp20) cc_final: 0.5803 (pp20)
REVERT: A 1748 LEU cc_start: 0.8410 (tp) cc_final: 0.8149 (tp)
REVERT: A 1811 ILE cc_start: 0.7521 (pt) cc_final: 0.7314 (pt)
REVERT: A 1825 MET cc_start: 0.7574 (mtm) cc_final: 0.7363 (mtt)
REVERT: A 1837 MET cc_start: 0.6516 (mtt) cc_final: 0.5463 (mtt)
REVERT: A 1860 MET cc_start: 0.1118 (ptt) cc_final: 0.0827 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 182
  average time/residue: 0.1334
  time to fit residues: 32.6553
Evaluate side-chains
  142 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 142
  time to evaluate  : 0.487 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 2 optimal weight:    1.9990
   chunk 10 optimal weight:   20.0000
   chunk 128 optimal weight:    9.9990
   chunk 29 optimal weight:    8.9990
   chunk 53 optimal weight:    0.6980
   chunk 58 optimal weight:    8.9990
   chunk 109 optimal weight:    5.9990
   chunk 45 optimal weight:    2.9990
   chunk 41 optimal weight:    0.9990
   chunk 106 optimal weight:    5.9990
   chunk 30 optimal weight:    8.9990
   overall best weight:    2.5388

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1689 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4201 r_free = 0.4201 target = 0.088732 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.069469 restraints weight = 77831.731|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.071506 restraints weight = 56217.150|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3861 r_free = 0.3861 target = 0.073063 restraints weight = 43735.694|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3883 r_free = 0.3883 target = 0.074151 restraints weight = 36158.177|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3900 r_free = 0.3900 target = 0.075029 restraints weight = 31159.616|
|-----------------------------------------------------------------------------|
r_work (final): 0.3898
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6507
moved from start:          0.5374

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  11334  Z= 0.184
  Angle     :  0.930  11.754  15327  Z= 0.476
  Chirality :  0.050   0.227   1747
  Planarity :  0.006   0.083   1954
  Dihedral  :  6.992  33.131   1519
  Min Nonbonded Distance : 2.358

Molprobity Statistics.
  All-atom Clashscore : 25.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 15.85 %
    Favored  : 84.15 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.97 %
    Favored  : 99.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.57 %
    Cis-general     : 1.60 %
    Twisted Proline : 0.00 %
    Twisted General : 0.15 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.82 (0.22), residues: 1369
  helix: -0.56 (0.20), residues: 632
  sheet: -2.81 (0.49), residues: 100
  loop : -3.16 (0.24), residues: 637

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A1314 
 TYR   0.020   0.002   TYR A  47 
 PHE   0.021   0.002   PHE A 347 
 TRP   0.016   0.003   TRP A 138 
 HIS   0.011   0.001   HIS A1062 

Details of bonding type rmsd
  covalent geometry    : bond        0.00391 (11332)
  covalent geometry    : angle       0.92996 (15323)
  SS BOND              : bond        0.00300 (    2)
  SS BOND              : angle       1.53809 (    4)
  hydrogen bonds       : bond        0.05032 (  465)
  hydrogen bonds       : angle       5.95688 ( 1368)

*********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2738 Ramachandran restraints generated.
    1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2738 Ramachandran restraints generated.
    1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 175
  time to evaluate  : 0.465 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   48 GLN cc_start: 0.8756 (mp10) cc_final: 0.8532 (mp10)
REVERT: A   64 LEU cc_start: 0.7564 (tp) cc_final: 0.7364 (tp)
REVERT: A  171 LEU cc_start: 0.8273 (mt) cc_final: 0.8059 (mt)
REVERT: A  190 MET cc_start: 0.8407 (ttp) cc_final: 0.7946 (tmm)
REVERT: A  263 ARG cc_start: 0.4804 (tpt90) cc_final: 0.4329 (mtp180)
REVERT: A  279 ASN cc_start: 0.9443 (t0) cc_final: 0.8986 (p0)
REVERT: A  306 CYS cc_start: 0.7017 (m) cc_final: 0.6794 (m)
REVERT: A  324 MET cc_start: 0.1788 (ptt) cc_final: 0.1536 (ptp)
REVERT: A  335 HIS cc_start: 0.8257 (t-90) cc_final: 0.7551 (m90)
REVERT: A  506 ARG cc_start: 0.8182 (ttt180) cc_final: 0.7773 (mmt180)
REVERT: A  550 LYS cc_start: 0.8198 (ttpt) cc_final: 0.7612 (pttt)
REVERT: A  965 TYR cc_start: 0.8915 (m-80) cc_final: 0.8460 (m-80)
REVERT: A 1317 MET cc_start: 0.7074 (mtp) cc_final: 0.6812 (mtp)
REVERT: A 1337 ASP cc_start: 0.8886 (p0) cc_final: 0.8650 (p0)
REVERT: A 1346 MET cc_start: 0.7689 (mmm) cc_final: 0.7336 (mmm)
REVERT: A 1358 ARG cc_start: 0.7442 (mtt180) cc_final: 0.6977 (mtt-85)
REVERT: A 1564 GLU cc_start: 0.8654 (mt-10) cc_final: 0.8272 (mt-10)
REVERT: A 1664 SER cc_start: 0.7680 (t) cc_final: 0.7464 (p)
REVERT: A 1668 ASN cc_start: 0.7982 (t0) cc_final: 0.7635 (t0)
REVERT: A 1682 TYR cc_start: 0.8313 (m-10) cc_final: 0.8079 (m-10)
REVERT: A 1692 TYR cc_start: 0.8020 (t80) cc_final: 0.7744 (t80)
REVERT: A 1748 LEU cc_start: 0.8459 (tp) cc_final: 0.8188 (tp)
REVERT: A 1782 MET cc_start: 0.3635 (mpp) cc_final: 0.3419 (mpp)
REVERT: A 1837 MET cc_start: 0.6712 (mtt) cc_final: 0.5816 (mtt)
REVERT: A 1860 MET cc_start: 0.1203 (ptt) cc_final: 0.0919 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 175
  average time/residue: 0.1179
  time to fit residues: 27.8506
Evaluate side-chains
  129 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 129
  time to evaluate  : 0.303 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 92 optimal weight:    0.9990
   chunk 24 optimal weight:   20.0000
   chunk 43 optimal weight:    1.9990
   chunk 23 optimal weight:    1.9990
   chunk 123 optimal weight:    6.9990
   chunk 122 optimal weight:    0.9980
   chunk 70 optimal weight:    0.7980
   chunk 64 optimal weight:    0.0870
   chunk 114 optimal weight:    1.9990
   chunk 37 optimal weight:    1.9990
   chunk 81 optimal weight:    6.9990
   overall best weight:    0.9762

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 514 ASN
** A 786 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1685 GLN
** A1689 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4258 r_free = 0.4258 target = 0.090846 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.071884 restraints weight = 82005.953|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.074006 restraints weight = 58035.722|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3926 r_free = 0.3926 target = 0.075640 restraints weight = 44673.877|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3950 r_free = 0.3950 target = 0.076826 restraints weight = 36382.609|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3964 r_free = 0.3964 target = 0.077550 restraints weight = 30892.782|
|-----------------------------------------------------------------------------|
r_work (final): 0.3934
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6474
moved from start:          0.5730

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  11334  Z= 0.161
  Angle     :  0.905  11.780  15327  Z= 0.463
  Chirality :  0.049   0.212   1747
  Planarity :  0.006   0.074   1954
  Dihedral  :  6.840  33.696   1519
  Min Nonbonded Distance : 2.387

Molprobity Statistics.
  All-atom Clashscore : 21.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 15.41 %
    Favored  : 84.59 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.24 %
    Favored  : 99.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.57 %
    Cis-general     : 1.60 %
    Twisted Proline : 0.00 %
    Twisted General : 0.23 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.75 (0.22), residues: 1369
  helix: -0.45 (0.20), residues: 630
  sheet: -2.93 (0.48), residues: 106
  loop : -3.14 (0.24), residues: 633

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A1314 
 TYR   0.042   0.002   TYR A 637 
 PHE   0.038   0.002   PHE A 351 
 TRP   0.020   0.003   TRP A 138 
 HIS   0.011   0.001   HIS A1062 

Details of bonding type rmsd
  covalent geometry    : bond        0.00336 (11332)
  covalent geometry    : angle       0.90516 (15323)
  SS BOND              : bond        0.00192 (    2)
  SS BOND              : angle       1.39272 (    4)
  hydrogen bonds       : bond        0.04868 (  465)
  hydrogen bonds       : angle       5.87461 ( 1368)

********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2738 Ramachandran restraints generated.
    1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2738 Ramachandran restraints generated.
    1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 178
  time to evaluate  : 0.405 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   48 GLN cc_start: 0.8823 (mp10) cc_final: 0.8552 (mp10)
REVERT: A   64 LEU cc_start: 0.7420 (tp) cc_final: 0.7065 (tp)
REVERT: A  171 LEU cc_start: 0.8142 (mt) cc_final: 0.7910 (mt)
REVERT: A  190 MET cc_start: 0.8440 (ttp) cc_final: 0.8016 (tmm)
REVERT: A  263 ARG cc_start: 0.4998 (tpt90) cc_final: 0.4547 (mtm110)
REVERT: A  335 HIS cc_start: 0.8246 (t-90) cc_final: 0.7524 (m90)
REVERT: A  506 ARG cc_start: 0.8096 (ttt180) cc_final: 0.7706 (mmt180)
REVERT: A  575 ASP cc_start: 0.9020 (m-30) cc_final: 0.8805 (p0)
REVERT: A  965 TYR cc_start: 0.8850 (m-80) cc_final: 0.8413 (m-80)
REVERT: A 1337 ASP cc_start: 0.8946 (p0) cc_final: 0.8693 (p0)
REVERT: A 1346 MET cc_start: 0.7573 (mmm) cc_final: 0.7231 (mmm)
REVERT: A 1358 ARG cc_start: 0.7464 (mtt180) cc_final: 0.6950 (mtt-85)
REVERT: A 1564 GLU cc_start: 0.8633 (mt-10) cc_final: 0.8216 (mt-10)
REVERT: A 1664 SER cc_start: 0.7674 (t) cc_final: 0.7449 (p)
REVERT: A 1682 TYR cc_start: 0.8458 (m-10) cc_final: 0.8158 (m-10)
REVERT: A 1782 MET cc_start: 0.3190 (mpp) cc_final: 0.2983 (mpp)
REVERT: A 1808 MET cc_start: 0.6068 (mmt) cc_final: 0.5867 (mmm)
REVERT: A 1837 MET cc_start: 0.6757 (mtt) cc_final: 0.5952 (mtt)
REVERT: B  348 ARG cc_start: 0.8574 (mtt180) cc_final: 0.8161 (tpt90)
REVERT: B  362 MET cc_start: 0.7599 (mmp) cc_final: 0.7288 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 178
  average time/residue: 0.1184
  time to fit residues: 28.8914
Evaluate side-chains
  136 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 136
  time to evaluate  : 0.364 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 117 optimal weight:    9.9990
   chunk 103 optimal weight:    1.9990
   chunk 64 optimal weight:    0.0030
   chunk 81 optimal weight:    0.8980
   chunk 82 optimal weight:    0.9990
   chunk 108 optimal weight:    0.9990
   chunk 3 optimal weight:    2.9990
   chunk 48 optimal weight:    9.9990
   chunk 78 optimal weight:    4.9990
   chunk 31 optimal weight:    0.6980
   chunk 110 optimal weight:    0.9980
   overall best weight:    0.7192

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A  84 GLN
** A 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 301 GLN
A 514 ASN
** A 786 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1689 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1693 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4274 r_free = 0.4274 target = 0.091958 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3889 r_free = 0.3889 target = 0.073338 restraints weight = 79170.360|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3928 r_free = 0.3928 target = 0.075401 restraints weight = 57204.586|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3958 r_free = 0.3958 target = 0.076945 restraints weight = 44537.598|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3980 r_free = 0.3980 target = 0.078121 restraints weight = 36856.255|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.3991 r_free = 0.3991 target = 0.078684 restraints weight = 31657.399|
|-----------------------------------------------------------------------------|
r_work (final): 0.3967
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6444
moved from start:          0.6112

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  11334  Z= 0.157
  Angle     :  0.890  11.802  15327  Z= 0.457
  Chirality :  0.049   0.185   1747
  Planarity :  0.006   0.066   1954
  Dihedral  :  6.651  34.036   1519
  Min Nonbonded Distance : 2.410

Molprobity Statistics.
  All-atom Clashscore : 21.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.97 %
    Favored  : 85.03 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.40 %
    Favored  : 99.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.57 %
    Cis-general     : 1.60 %
    Twisted Proline : 0.00 %
    Twisted General : 0.23 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.63 (0.22), residues: 1369
  helix: -0.38 (0.20), residues: 633
  sheet: -2.26 (0.54), residues: 100
  loop : -3.18 (0.24), residues: 636

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A1314 
 TYR   0.029   0.002   TYR A 637 
 PHE   0.041   0.002   PHE A1766 
 TRP   0.014   0.003   TRP A 138 
 HIS   0.011   0.001   HIS A1062 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 (11332)
  covalent geometry    : angle       0.88999 (15323)
  SS BOND              : bond        0.00202 (    2)
  SS BOND              : angle       1.32352 (    4)
  hydrogen bonds       : bond        0.04720 (  465)
  hydrogen bonds       : angle       5.67792 ( 1368)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2145.68 seconds
wall clock time: 37 minutes 58.32 seconds (2278.32 seconds total)